Speaking publicly for first time since leaving the church in 2009, Haggis also provides a glimpse into the controversial church.

"I was in a cult for 34 years," he told the New Yorker of his time in the church. "Everyone else could see it. I don't know why I couldn't."

Haggis was a practicing Scientologist along with the likes of celebrities like John Travolta and Tom Cruise, who remain in the church.

Haggis, who was a screenwriter for "Million Dollar Baby" and "Crash," which he also directed said Scientology started out for him as something that provided a sense of belonging.

"There was a feeling of camaraderie that was something I'd never experienced; all these atheists looking for something to believe in, and all these loners looking for a club to join," Haggis said in the New Yorker article.

L. Ron Hubbard founded the church in 1952 as a "religion that offers a precise path leading to a complete and certain understanding of one's true spiritual nature and one's relationship to self, family, groups, Mankind, all life forms, the material universe, the spiritual universe and the Supreme Being," according to the church's website.

There are more than 8,600 churches and missions with millions of members in 165 countries, according to the Church of Scientology website.

"It is unfortunate that The New Yorker chose to introduce its readers to Scientology through the eyes of an apostate, someone religious scholars unanimously denounce as unreliable, rather than take advantage of the Church's invitation to experience its practices and humanitarian works firsthand," the church replied to the article in a statement to ABC News. "The article is little more than a regurgitation of old allegations that have
long been disproved. It is disappointing that a magazine with the reputation of The New Yorker chose to reprint these sensationalist claims from disaffected former members hardly worthy of a tabloid."

Haggis Resigns Over Prop. 8

For Haggis, the church's declining to publicly denounce Proposition 8, the measure that banned same-sex marriages in California, conflicted with his view on the issue and eventually led to his parting ways with the church.

The tension started in 2008, according to the New Yorker, when a staff member at a Scientologist church in San Diego signed the church's name to a pro-Prop. 8 online petition, according to the New Yorker.

Tommy Davis, chief spokesman for the Church of Scientology International, told Haggis at the time that the listing was an error and that the church "avoids taking overt political stands," the magazine wrote.

Haggis said he was vehemently opposed to Prop. 8 because his youngest daughter, Katy, from his first marriage, "lost the friendship of a fellow-Scientologist after revealing that she was gay," according to the New Yorker.

Davis also told the magazine that he told Haggis that Katy's friend ended the friendship not because Katy was "lesbian but because Katy lied about it."

Davis told Haggis that making a public statement on the issue would bring "more attention than if we leave it be," according to the article.

Haggis told Davis in a letter in February 2009 that this wasn't a public relations issue but "a moral issue," later conceding to Davis, however, "You were right: Nothing happened -- it didn't flap -- at least not every much. But I feel we shamed ourselves," the magazine reported.

Six months later, the issue still resonated with Haggis.

"Silence is consent, Tommy. I refuse to consent. I hereby resign my membership in the Church of Scientology," Haggis wrote to Davis in a letter dated Aug. 19, 2009, according to the New Yorker interview.

The New Yorker writes that the incident sparked Haggis' research and exploration of the church beyond official documents.

Haggis looked for information online about the church and read an expose by the St. Petersburg Times that reported allegations of physical violence among church senior executives and other Scientologists, according to the article.

Other Allegations by Former Members

The New Yorker article highlights several other revelations about Haggis' relationship with the church and negative allegations against the church by former members including:

"Disconnection" -- A number of former scientologists have alleged that the church orders member to disconnect from friends or family who have left and who take positions critical of the church. Haggis told the New Yorker that his wife was ordered to disconnect from her parents after that left the church. Scicentology spokesmen deny any formal policy of "disconnection," although they say many members will choose to cut off connections with "apostates."

Cost of coursework -- Haggis told the magazine that he reached one of the highest levels in the church, Operating Thetan VII, by purchasing incentives and "bundled hours of auditing." The article says that, according to a professor who researched the church, the cost of taking courses could run as high as half a million. The church told the New Yorker that donations are "requested" and begin at $50 and could never possibly reach that amount suggested."

"E-meter" - The New Yorker describes this device as an electropsychometer that "measures bodily changes in electrical resistance that occurs when a person answers questions by an auditor." Haggis told the New Yorker that he found it to be "responsive."

"Purification rundown" -- Haggis told the Scientology magazine, Celebrity, in 1986 that he experienced the purification rundown - a program "intended to eliminate body toxins" that were a barrier to "spiritual well-being," the New Yorker described. The rundown included vitamins and sauna sessions.

Alleged physical beating by Church Leader David Miscavige -- The New Yorker interviewed former church members who alleged that Miscavige physically struck staff members. Church officials have told the New Yorker that those are making the allegations are "discredited individuals" who were demoted for incompetence or expelled for corruption.

FBI Probe on Human Trafficking?

Aside from presenting Paul Haggis' account of his time in Scientology, the New Yorker article also alleges an "investigation" by the FBI in December of 2009.

The New Yorker says FBI agents who worked on a human trafficking task force went to Clearwater, Fla., to interview former members about allegations that members of the Scientology staff, or "Sea Org," could be subjected to what some defectors have called "punitive Reeducation" during sometimes years-long "confinement" at so-called rehabilitation project force locations involving "manual labor and extensive spiritual work."

A spokesman told the New Yorker that stays at the rehabilitation project force locations were "entirely voluntary" and that members could leave the facilities at any time.

Contacted by ABC News, the FBI declined to comment, saying that "by policy we can neither confirm nor deny the existence of an investigation."

The church, in the statement to ABC News, also wrote, "Moreover, the subject of the alleged investigation was recently raised in a lawsuit by the same individuals who are the sources for the article and the complaint was resoundingly dismissed by a Federal District Court Judge. The New Yorker was aware of this fact but irresponsibly sought to use the claim of an "investigation" to garner headlines for an otherwise stale article containing nothing but rehashed unfounded allegations."

Church's Full Response

"It is unfortunate that The New Yorker chose to introduce its readers to
Scientology through the eyes of an apostate, someone religious scholars
unanimously denounce as unreliable, rather than take advantage of the
Church's invitation to experience its practices and humanitarian works
firsthand. The New Yorker doesn't mention Scientology's global human
rights initiative, which has educated millions on human rights. Or its
"Truth About Drug" crusade, teaching millions how to live drug-free. Or
its global Volunteer Ministers program, whose work in Haiti alone has
been hailed by the international community. Or its dozens of new
Churches bringing Scientology's life saving technology to communities
around the world. Indeed the newest Church opened just this last week in
Melbourne, Australia.

"The one grain of truth in the article is its acknowledgement of the positive
effect Scientology has had on the lives of its adherents and the world at
large—that is the message of Scientology.

"The article is little more than a regurgitation of old allegations that have
long been disproved. It is disappointing that a magazine with the
reputation of The New Yorker chose to reprint these sensationalist claims
from disaffected former members hardly worthy of a tabloid. As for the
claim that the Church is the subject of a federal investigation, the Church
has never been advised of any government investigation, a fact The New
Yorker knew before it went to print. Moreover, the subject of the alleged
investigation was recently raised in a lawsuit by the same individuals who
are the sources for the article and the complaint was resoundingly
dismissed by a Federal District Court Judge. The New Yorker was aware of

this fact but irresponsibly sought to use the claim of an "investigation" to
garner headlines for an otherwise stale article containing nothing but
rehashed unfounded allegations.

"Anyone who wants to know the true story of Scientology should find out
for themselves by coming to a Church of Scientology, whose doors are
always open, or going to the Church's website, www.Scientology.org.